It turns out that atheist parents don't attempt to raise their children in an "atheist tradition" the way religious parents do with religious traditions. Rice University sociologist Elaine Ecklund surveyed over 2,000 scientists and found that half expressed "no religious identity." She pulled 275 of these atheists, and found that at least 17% had brought their children to a religious service in the past year.

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From a release about the study:

The individuals surveyed cited personal and social reasons for integrating religion into their lives, including:

Scientific identity – Study participants wish to expose their children to all sources of knowledge (including religion) and allow them to make their own choices about a religious identity.
Spousal influence – Study participants are involved in a religious institution because of influence from their spouse or partner.
Desire for community – Study participants want a sense of moral community and behavior, even if they don't agree with the religious reasoning.
Ecklund said one of the most interesting findings was discovering that not only do some atheist scientists wish to expose their children to religious institutions, but they also cite their scientific identity as reason for doing so.

"We thought that these individuals might be less inclined to introduce their children to religious traditions, but we found the exact opposite to be true," Ecklund said. "They want their children to have choices, and it is more consistent with their science identity to expose their children to all sources of knowledge."

One study participant raised in a strongly Catholic home said he came to believe later that science and religion were not compatible. He said what he wants to pass on to his daughter – more than the belief that science and religion are not compatible – is the ability to make her own decisions in a thoughtful, intellectual way.